Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate AO356_25515 AO356_25515 3-ketoacyl-ACP reductase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25515 Length = 255 Score = 166 bits (420), Expect = 4e-46 Identities = 97/245 (39%), Positives = 144/245 (58%), Gaps = 5/245 (2%) Query: 6 KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGA 65 +TV+VTG ++GIGRA A +GARVVI +D G A A ++A+E+ A G AVG Sbjct: 10 QTVLVTGGAQGIGRAIVEAFALRGARVVI----ADLGLARAEAVADELTAVGCQVQAVGV 65 Query: 66 DAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAYFTV 125 D AD + ++++A + G +D LV+NAG P F ++ + +T+ NL+ ++ Sbjct: 66 DLADATAIFEMMSALEQRLGRLDTLVHNAGYFPLTPFAEITPAMLERTLAVNLSALFWLT 125 Query: 126 QAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIRCN 185 QAA + QGRG ++ S V +HY +KAG+ +++ A+ L +R N Sbjct: 126 QAALPMFRRQGRGCVLVTSSVTGPRVAYPGLSHYAASKAGVNGFIRNAALELAAENVRVN 185 Query: 186 AVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGASL 245 V PG IAT +L D E + + RVPLGRLG+P D+AG ++FLAS +A YVTG +L Sbjct: 186 GVEPGMIATPA-MANLGDDEVNQDIARRVPLGRLGQPSDIAGAMLFLASSLASYVTGQTL 244 Query: 246 LVDGG 250 +VDGG Sbjct: 245 VVDGG 249 Lambda K H 0.319 0.136 0.383 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 163 Number of extensions: 6 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 256 Length of database: 255 Length adjustment: 24 Effective length of query: 232 Effective length of database: 231 Effective search space: 53592 Effective search space used: 53592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory